Rice is Thailand's staple grain and one of the country's main exports. But India and Vietnam surpassed Thailand as the world's top rice exporters in 2012 as the Thai government stockpiled rice to avoid even bigger losses.
The IMF also said lack of data about the rice purchasing program has diminished confidence in Thailand's public finances.
Thai officials said in the report that a reduction in the pledging prices or a purchase limit might be necessary to sustain the policy but insisted the scheme was aimed at reducing economic inequality in the Southeast Asian nation.
The IMF suggested the Thai government replace rice price pledging and other generalized subsidies with programs that are targeted at vulnerable groups, including low-income farming households.
Thai governments have intervened in the rice market through a variety of means since the early 1960s to help farmers, but the current scheme has its roots in the populist policies of Yingluck's brother, former prime minister Thaksin Shinawatra, who won landslide victories in two elections before he was ousted in a 2006 coup.
The scheme has been dogged by corruption and accusations the government has hidden its true cost.